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Yorodumi- EMDB-0246: Leucine-zippered human insulin receptor ectodomain with single bo... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-0246 | |||||||||||||||
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Title | Leucine-zippered human insulin receptor ectodomain with single bound insulin - "lower" membrane-proximal part | |||||||||||||||
Map data | insulin bound to insulin receptor ectodomain - "lower" membrane-proximal part | |||||||||||||||
Sample |
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Function / homology | Function and homology information regulation of female gonad development / positive regulation of meiotic cell cycle / protein localization to nuclear periphery / Activation of the AP-1 family of transcription factors / positive regulation of developmental growth / response to amino acid starvation / insulin-like growth factor II binding / mediator complex binding / negative regulation of ribosomal protein gene transcription by RNA polymerase II / positive regulation of cellular response to amino acid starvation ...regulation of female gonad development / positive regulation of meiotic cell cycle / protein localization to nuclear periphery / Activation of the AP-1 family of transcription factors / positive regulation of developmental growth / response to amino acid starvation / insulin-like growth factor II binding / mediator complex binding / negative regulation of ribosomal protein gene transcription by RNA polymerase II / positive regulation of cellular response to amino acid starvation / male sex determination / exocrine pancreas development / insulin receptor complex / insulin-like growth factor I binding / insulin receptor activity / nitrogen catabolite activation of transcription from RNA polymerase II promoter / positive regulation of protein-containing complex disassembly / cargo receptor activity / dendritic spine maintenance / insulin binding / PTB domain binding / neuronal cell body membrane / adrenal gland development / Signaling by Insulin receptor / IRS activation / amyloid-beta clearance / activation of protein kinase activity / positive regulation of respiratory burst / TFIID-class transcription factor complex binding / regulation of embryonic development / positive regulation of receptor internalization / transport across blood-brain barrier / amino acid biosynthetic process / insulin receptor substrate binding / positive regulation of transcription initiation by RNA polymerase II / positive regulation of RNA polymerase II transcription preinitiation complex assembly / epidermis development / positive regulation of glycogen biosynthetic process / Signal attenuation / phosphatidylinositol 3-kinase binding / heart morphogenesis / dendrite membrane / Insulin receptor recycling / insulin-like growth factor receptor binding / cellular response to amino acid starvation / receptor-mediated endocytosis / neuron projection maintenance / activation of protein kinase B activity / positive regulation of glycolytic process / Insulin receptor signalling cascade / positive regulation of mitotic nuclear division / learning / caveola / positive regulation of glucose import / positive regulation of MAP kinase activity / receptor internalization / memory / receptor protein-tyrosine kinase / cellular response to growth factor stimulus / peptidyl-tyrosine phosphorylation / RNA polymerase II transcription regulator complex / cellular response to insulin stimulus / male gonad development / cell surface receptor protein tyrosine kinase signaling pathway / : / positive regulation of nitric oxide biosynthetic process / late endosome / glucose homeostasis / insulin receptor signaling pathway / amyloid-beta binding / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / DNA-binding transcription activator activity, RNA polymerase II-specific / protein tyrosine kinase activity / transcription regulator complex / RNA polymerase II-specific DNA-binding transcription factor binding / sequence-specific DNA binding / positive regulation of MAPK cascade / protein autophosphorylation / lysosome / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / receptor complex / endosome membrane / DNA-binding transcription factor activity, RNA polymerase II-specific / carbohydrate metabolic process / intracellular signal transduction / positive regulation of cell migration / positive regulation of protein phosphorylation / symbiont entry into host cell / G protein-coupled receptor signaling pathway / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / axon / protein domain specific binding / external side of plasma membrane / protein phosphorylation / chromatin binding / positive regulation of cell population proliferation / protein-containing complex binding / GTP binding / regulation of DNA-templated transcription Similarity search - Function | |||||||||||||||
Biological species | Homo sapiens (human) / Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) | |||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.2 Å | |||||||||||||||
Authors | Weis F / Menting JG / Margetts MB / Chan SJ / Xu Y / Tennagels N / Wohlfart P / Langer T / Mueller CW / Dreyer MK / Lawrence MC | |||||||||||||||
Funding support | Australia, United States, 4 items
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Citation | Journal: Nat Commun / Year: 2018 Title: The signalling conformation of the insulin receptor ectodomain. Authors: Felix Weis / John G Menting / Mai B Margetts / Shu Jin Chan / Yibin Xu / Norbert Tennagels / Paulus Wohlfart / Thomas Langer / Christoph W Müller / Matthias K Dreyer / Michael C Lawrence / Abstract: Understanding the structural biology of the insulin receptor and how it signals is of key importance in the development of insulin analogs to treat diabetes. We report here a cryo-electron microscopy ...Understanding the structural biology of the insulin receptor and how it signals is of key importance in the development of insulin analogs to treat diabetes. We report here a cryo-electron microscopy structure of a single insulin bound to a physiologically relevant, high-affinity version of the receptor ectodomain, the latter generated through attachment of C-terminal leucine zipper elements to overcome the conformational flexibility associated with ectodomain truncation. The resolution of the cryo-electron microscopy maps is 3.2 Å in the insulin-binding region and 4.2 Å in the membrane-proximal region. The structure reveals how the membrane proximal domains of the receptor come together to effect signalling and how insulin's negative cooperativity of binding likely arises. Our structure further provides insight into the high affinity of certain super-mitogenic insulins. Together, these findings provide a new platform for insulin analog investigation and design. | |||||||||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_0246.map.gz | 2.5 MB | EMDB map data format | |
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Header (meta data) | emd-0246-v30.xml emd-0246.xml | 17.4 KB 17.4 KB | Display Display | EMDB header |
Images | emd_0246.png | 110.5 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-0246 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-0246 | HTTPS FTP |
-Related structure data
Related structure data | 6hn4MC 0247C 6hn5C M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_0246.map.gz / Format: CCP4 / Size: 91.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | insulin bound to insulin receptor ectodomain - "lower" membrane-proximal part | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.04 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Leucine zippered human insulin receptor ectodomain (IR-A isoform,...
Entire | Name: Leucine zippered human insulin receptor ectodomain (IR-A isoform, "deltabeta" mutant) in complex with insulin and two Fv 83-7 modules : "lower" membrane-proximal part |
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Components |
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-Supramolecule #1: Leucine zippered human insulin receptor ectodomain (IR-A isoform,...
Supramolecule | Name: Leucine zippered human insulin receptor ectodomain (IR-A isoform, "deltabeta" mutant) in complex with insulin and two Fv 83-7 modules : "lower" membrane-proximal part type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 Details: Note: Attached to the leucine-zippered insulin receptor ectodomain are two Fv 83-7 modules. One of these is present within this map volume but it is very poorly ordered and thus left ...Details: Note: Attached to the leucine-zippered insulin receptor ectodomain are two Fv 83-7 modules. One of these is present within this map volume but it is very poorly ordered and thus left completely unmodelled. See the manuscript for further details. |
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Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Cricetulus griseus (Chinese hamster) / Recombinant cell: Lec8 / Recombinant plasmid: pEE14 |
-Macromolecule #1: Insulin receptor,Insulin receptor,General control protein GCN4
Macromolecule | Name: Insulin receptor,Insulin receptor,General control protein GCN4 type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: receptor protein-tyrosine kinase |
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Source (natural) | Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c |
Molecular weight | Theoretical: 106.728211 KDa |
Recombinant expression | Organism: Cricetulus griseus (Chinese hamster) |
Sequence | String: HLYPGEVCPG MDIRNNLTRL HELENCSVIE GHLQILLMFK TRPEDFRDLS FPKLIMITDY LLLFRVYGLE SLKDLFPNLT VIRGSRLFF NYALVIFEMV HLKELGLYNL MNITRGSVRI EKNNELCYLA TIDWSRILDS VEDNHIVLNK DDNEECGDIC P GTAKGKTN ...String: HLYPGEVCPG MDIRNNLTRL HELENCSVIE GHLQILLMFK TRPEDFRDLS FPKLIMITDY LLLFRVYGLE SLKDLFPNLT VIRGSRLFF NYALVIFEMV HLKELGLYNL MNITRGSVRI EKNNELCYLA TIDWSRILDS VEDNHIVLNK DDNEECGDIC P GTAKGKTN CPATVINGQF VERCWTHSHC QKVCPTICKS HGCTAEGLCC HSECLGNCSQ PDDPTKCVAC RNFYLDGRCV ET CPPPYYH FQDWRCVNFS FCQDLHHKCK NSRRQGCHQY VIHNNKCIPE CPSGYTMNSS NLLCTPCLGP CPKVCHLLEG EKT IDSVTS AQELRGCTVI NGSLIINIRG GNNLAAELEA NLGLIEEISG YLKIRRSYAL VSLSFFRKLR LIRGETLEIG NYSF YALDN QNLRQLWDWS KHNLTTTQGK LFFHYNPKLC LSEIHKMEEV SGTKGRQERN DIALKTNGDK ASCENELLKF SYIRT SFDK ILLRWEPYWP PDFRDLLGFM LFYKEAPYQN VTEFDGQDAC GSNSWTVVDI DPPLRSNDPK SQNHPGWLMR GLKPWT QYA IFVKTLVTFS DERRTYGAKS DIIYVQTDAT NPSVPLDPIS VSNSSSQIIL KWKPPSDPNG NITHYLVFWE RQAEDSE LF ELDYCLKGLK LPSRTWSPPF ESEDSQKHNQ SEYEDSAGEC CSCPKTDSQI LKELEESSFR KTFEDYLHNV VFVPRPSR K RRSLGDVGNA GNNEEHRPFE KVVNKESLVI SGLRHFTGYR IELQACNQDT PEERCSVAAY VSARTMPEAK ADDIVGPVT HEIFENNVVH LMWQEPKEPN GLIVLYEVSY RRYGDEELHL CVSRKHFALE RGCRLRGLSP GNYSVRIRAT SLAGNGSWTE PTYFYVTDY LDVPSNIARM KQLEDKVEEL LSKNYHLENE VARLKKLVGE R |
-Macromolecule #2: 2-acetamido-2-deoxy-beta-D-glucopyranose
Macromolecule | Name: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 2 / Number of copies: 6 / Formula: NAG |
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Molecular weight | Theoretical: 221.208 Da |
Chemical component information | ChemComp-NAG: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.094 mg/mL | |||||||||
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Buffer | pH: 7.5 Component:
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Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 283.15 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 130000 |
Specialist optics | Energy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Digitization - Frames/image: 1-20 / Number grids imaged: 1 / Number real images: 2287 / Average exposure time: 16.0 sec. / Average electron dose: 1.85 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Particle selection | Number selected: 747074 |
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CTF correction | Software - Name: Gctf |
Startup model | Type of model: PDB ENTRY PDB model - PDB ID: Details: symmetrised domains L1, CR and L2 bound to Fv 83-7 |
Initial angle assignment | Type: PROJECTION MATCHING / Software - Name: RELION (ver. 2.1) |
Final 3D classification | Number classes: 6 / Software - Name: RELION (ver. 2.1) Details: performed with partial signal subtraction of the "upper" part. |
Final angle assignment | Type: PROJECTION MATCHING / Software - Name: RELION (ver. 2.1) |
Final reconstruction | Number classes used: 2 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.1) / Number images used: 98481 |